Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 852YY

Calculation Name: 3QSQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QSQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9IFX1

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2670682.690587
FMO2-HF: Nuclear repulsion 2585013.561963
FMO2-HF: Total energy -85669.128624
FMO2-MP2: Total energy -85920.535435


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:430:GLU)


Summations of interaction energy for fragment #1(A:430:GLU)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-50.115-56.13432.467-14.732-11.7170.059
Interaction energy analysis for fragmet #1(A:430:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.863 / q_NPA : -0.919
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A432PHE00.0120.0182.392-6.201-1.9681.764-2.281-3.7170.012
4A433ARG10.7950.8975.434-27.290-27.2900.0000.0000.0000.000
5A434VAL0-0.020-0.0159.2760.8480.8480.0000.0000.0000.000
6A435LEU0-0.0030.00711.954-1.057-1.0570.0000.0000.0000.000
7A436LEU0-0.021-0.00913.7330.0670.0670.0000.0000.0000.000
8A437THR00.0340.01817.177-0.651-0.6510.0000.0000.0000.000
9A438VAL00.0220.01720.6880.2200.2200.0000.0000.0000.000
10A439GLY00.0200.01522.993-0.350-0.3500.0000.0000.0000.000
11A440PRO0-0.023-0.02525.230-0.245-0.2450.0000.0000.0000.000
12A441PRO00.0010.00827.9560.2830.2830.0000.0000.0000.000
13A442MET0-0.0160.00326.727-0.060-0.0600.0000.0000.0000.000
14A443ALA00.0480.03529.961-0.093-0.0930.0000.0000.0000.000
15A444PRO0-0.019-0.01332.0190.2360.2360.0000.0000.0000.000
16A445ASN0-0.049-0.01329.847-0.256-0.2560.0000.0000.0000.000
17A446THR00.024-0.00733.101-0.006-0.0060.0000.0000.0000.000
18A447ALA00.016-0.00532.9620.1600.1600.0000.0000.0000.000
19A448ASN0-0.0250.00533.9940.0480.0480.0000.0000.0000.000
20A449SER0-0.0180.00034.072-0.208-0.2080.0000.0000.0000.000
21A450GLN00.0580.01834.0570.1540.1540.0000.0000.0000.000
22A451ASN0-0.049-0.03227.5270.2610.2610.0000.0000.0000.000
23A452TRP0-0.016-0.01531.002-0.160-0.1600.0000.0000.0000.000
24A453VAL00.0150.00926.9470.3650.3650.0000.0000.0000.000
25A454ASN0-0.047-0.05626.808-0.801-0.8010.0000.0000.0000.000
26A455LYS10.8000.90028.056-8.803-8.8030.0000.0000.0000.000
27A456THR00.013-0.00829.3440.2300.2300.0000.0000.0000.000
28A457ILE00.0400.01326.2950.2850.2850.0000.0000.0000.000
29A458VAL0-0.015-0.00128.6600.2200.2200.0000.0000.0000.000
30A459PRO0-0.0010.01830.880-0.022-0.0220.0000.0000.0000.000
31A460PRO0-0.006-0.01832.785-0.220-0.2200.0000.0000.0000.000
32A461GLU-1-0.823-0.91836.0227.9827.9820.0000.0000.0000.000
33A462ASN0-0.085-0.03637.6420.0230.0230.0000.0000.0000.000
34A463GLN0-0.0050.01333.8120.2840.2840.0000.0000.0000.000
35A464TYR00.030-0.00229.3040.1340.1340.0000.0000.0000.000
36A465THR00.0100.01926.9710.0310.0310.0000.0000.0000.000
37A466VAL0-0.0020.00421.7810.1330.1330.0000.0000.0000.000
38A467LYS10.8110.91122.163-11.626-11.6260.0000.0000.0000.000
39A468ILE00.0160.00515.7850.2380.2380.0000.0000.0000.000
40A469GLY00.0480.01115.838-0.214-0.2140.0000.0000.0000.000
41A470ILE00.0150.02413.1600.5310.5310.0000.0000.0000.000
42A471ASP-1-0.811-0.87716.19414.90414.9040.0000.0000.0000.000
43A472LEU0-0.004-0.00419.961-0.027-0.0270.0000.0000.0000.000
44A473GLU-1-0.909-0.96622.14212.42012.4200.0000.0000.0000.000
45A474HIS10.7520.86717.468-14.517-14.5170.0000.0000.0000.000
46A475TYR00.0240.00817.6600.7650.7650.0000.0000.0000.000
47A476THR00.0140.01318.139-0.639-0.6390.0000.0000.0000.000
48A477THR0-0.063-0.04420.6390.1830.1830.0000.0000.0000.000
49A478MET00.0060.02121.7640.3390.3390.0000.0000.0000.000
50A479GLN00.0240.02022.710-0.499-0.4990.0000.0000.0000.000
51A480GLY00.0530.02223.307-0.455-0.4550.0000.0000.0000.000
52A481PHE0-0.016-0.02722.2970.5600.5600.0000.0000.0000.000
53A482THR0-0.010-0.01121.629-0.595-0.5950.0000.0000.0000.000
54A483PRO00.0000.00321.4470.7910.7910.0000.0000.0000.000
55A484VAL0-0.0160.00517.471-0.125-0.1250.0000.0000.0000.000
56A485GLU-1-0.820-0.90920.86512.63312.6330.0000.0000.0000.000
57A486SER0-0.032-0.02019.150-0.153-0.1530.0000.0000.0000.000
58A487VAL0-0.0050.00412.509-0.400-0.4000.0000.0000.0000.000
59A488SER0-0.0150.00814.982-0.184-0.1840.0000.0000.0000.000
60A489TRP00.0630.0128.9900.9020.9020.0000.0000.0000.000
61A490TYR0-0.014-0.0109.649-1.792-1.7920.0000.0000.0000.000
62A491THR00.0310.0016.4222.5002.5000.0000.0000.0000.000
63A492ALA00.0410.0224.465-2.878-2.876-0.001-0.0060.0050.000
64A493ASP-1-0.891-0.9366.40326.75926.7590.0000.0000.0000.000
65A494PHE0-0.029-0.0269.264-1.916-1.9160.0000.0000.0000.000
66A495GLN00.0380.03311.073-1.804-1.8040.0000.0000.0000.000
67A496PRO0-0.013-0.01611.0401.9901.9900.0000.0000.0000.000
68A497SER0-0.036-0.0188.3912.1232.1230.0000.0000.0000.000
69A498ASP-1-0.875-0.92210.18620.55320.5530.0000.0000.0000.000
70A499GLU-1-0.838-0.9229.44825.12325.1230.0000.0000.0000.000
71A500PRO0-0.0050.0185.7830.6350.6350.0000.0000.0000.000
72A501SER0-0.008-0.0277.138-4.072-4.0720.0000.0000.0000.000
73A502PRO0-0.017-0.0017.3523.9453.9450.0000.0000.0000.000
74A503ILE0-0.005-0.0016.6760.9340.9340.0000.0000.0000.000
75A504PRO00.011-0.0048.039-3.959-3.9590.0000.0000.0000.000
76A505GLY0-0.022-0.00810.988-0.078-0.0780.0000.0000.0000.000
77A506LEU0-0.047-0.01610.024-2.026-2.0260.0000.0000.0000.000
78A507TYR00.019-0.00113.2440.2200.2200.0000.0000.0000.000
79A508ALA00.0160.01216.246-0.721-0.7210.0000.0000.0000.000
80A509ARG10.8220.90317.553-16.041-16.0410.0000.0000.0000.000
81A510VAL00.0430.01822.238-0.222-0.2220.0000.0000.0000.000
82A511ASN00.0270.00825.990-0.058-0.0580.0000.0000.0000.000
83A512ASN0-0.011-0.01523.6760.3750.3750.0000.0000.0000.000
84A513THR0-0.0070.02224.1760.3190.3190.0000.0000.0000.000
85A514LYS10.9240.96518.512-15.882-15.8820.0000.0000.0000.000
86A515LYS10.8690.93321.142-12.533-12.5330.0000.0000.0000.000
87A516ALA00.0010.00318.447-0.281-0.2810.0000.0000.0000.000
88A517ASP-1-0.825-0.89813.78719.76719.7670.0000.0000.0000.000
89A518VAL0-0.024-0.02510.909-0.593-0.5930.0000.0000.0000.000
90A519TYR0-0.008-0.0309.4270.9040.9040.0000.0000.0000.000
91A520GLY00.0310.0267.7424.3394.3390.0000.0000.0000.000
92A521VAL0-0.068-0.0237.884-3.789-3.7890.0000.0000.0000.000
93A522GLN00.0330.0168.9181.0431.0430.0000.0000.0000.000
94A523GLN00.002-0.00811.441-1.445-1.4450.0000.0000.0000.000
95A524PHE00.0330.03714.230-0.044-0.0440.0000.0000.0000.000
96A525LYS10.8630.92016.236-16.394-16.3940.0000.0000.0000.000
97A526SER0-0.030-0.00919.784-0.296-0.2960.0000.0000.0000.000
98A527SER00.0350.02523.2870.0050.0050.0000.0000.0000.000
99A528HIS0-0.046-0.01926.250-0.144-0.1440.0000.0000.0000.000
100A529THR00.0060.00329.513-0.277-0.2770.0000.0000.0000.000
101A530ASN00.0300.00229.4940.4430.4430.0000.0000.0000.000
102A531ASN0-0.056-0.02229.4750.2460.2460.0000.0000.0000.000
103A532ARG10.9220.95129.153-9.369-9.3690.0000.0000.0000.000
104A533HIS10.8260.88424.136-11.084-11.0840.0000.0000.0000.000
105A534GLN00.0300.01423.502-0.561-0.5610.0000.0000.0000.000
106A535ILE0-0.023-0.02418.1990.3410.3410.0000.0000.0000.000
107A536THR0-0.028-0.02118.980-0.564-0.5640.0000.0000.0000.000
108A537SER0-0.0240.00515.4820.9750.9750.0000.0000.0000.000
109A538VAL0-0.032-0.02013.720-1.007-1.0070.0000.0000.0000.000
110A539PHE00.011-0.01113.0491.3741.3740.0000.0000.0000.000
111A540LEU00.0450.04711.049-1.581-1.5810.0000.0000.0000.000
112A541VAL0-0.026-0.02813.0471.4321.4320.0000.0000.0000.000
113A542ARG10.8810.93715.635-19.678-19.6780.0000.0000.0000.000
114A543VAL0-0.039-0.00717.3930.1420.1420.0000.0000.0000.000
115A544THR00.0540.02918.198-0.540-0.5400.0000.0000.0000.000
116A545THR0-0.065-0.04120.968-0.639-0.6390.0000.0000.0000.000
117A546SER00.0340.02024.7270.2580.2580.0000.0000.0000.000
118A547PHE0-0.053-0.02823.712-0.178-0.1780.0000.0000.0000.000
119A548GLN0-0.0010.00028.871-0.113-0.1130.0000.0000.0000.000
120A549VAL0-0.014-0.00128.0880.0500.0500.0000.0000.0000.000
121A550ILE00.0480.03931.0790.0230.0230.0000.0000.0000.000
122A551ASN0-0.068-0.06529.0000.4140.4140.0000.0000.0000.000
123A552TYR00.0560.03132.646-0.288-0.2880.0000.0000.0000.000
124A553THR0-0.030-0.01031.0970.1550.1550.0000.0000.0000.000
125A554SER00.008-0.02632.197-0.399-0.3990.0000.0000.0000.000
126A555TYR00.0350.03431.9380.1580.1580.0000.0000.0000.000
127A556PHE00.0350.01627.111-0.246-0.2460.0000.0000.0000.000
128A557ILE0-0.015-0.00732.580-0.185-0.1850.0000.0000.0000.000
129A558ARG10.9390.96034.841-8.448-8.4480.0000.0000.0000.000
130A559GLY00.0170.03437.623-0.090-0.0900.0000.0000.0000.000
131A560ALA00.0070.00141.1530.1120.1120.0000.0000.0000.000
132A561GLU-1-0.842-0.92742.5826.8956.8950.0000.0000.0000.000
133A562SER0-0.023-0.00545.002-0.110-0.1100.0000.0000.0000.000
134A563GLY0-0.002-0.00747.0730.0380.0380.0000.0000.0000.000
135A564SER00.003-0.00144.0600.0470.0470.0000.0000.0000.000
136A565ASN0-0.038-0.01143.2420.0910.0910.0000.0000.0000.000
137A566VAL00.001-0.00637.4370.1250.1250.0000.0000.0000.000
138A567SER0-0.005-0.00339.2850.1050.1050.0000.0000.0000.000
139A568ASN0-0.034-0.03235.4610.4260.4260.0000.0000.0000.000
140A569LEU0-0.0170.00429.971-0.163-0.1630.0000.0000.0000.000
141A570LYS10.8780.93233.357-7.794-7.7940.0000.0000.0000.000
142A571ILE00.0090.01730.8840.0920.0920.0000.0000.0000.000
143A572ARG10.8290.91333.446-8.400-8.4000.0000.0000.0000.000
144A573ASP-1-0.797-0.90236.1058.0768.0760.0000.0000.0000.000
145A574GLN00.0600.03437.7740.2180.2180.0000.0000.0000.000
146A575THR0-0.021-0.00235.4800.1970.1970.0000.0000.0000.000
147A576TYR0-0.021-0.02436.369-0.330-0.3300.0000.0000.0000.000
148A577HIS00.0130.01435.9940.2230.2230.0000.0000.0000.000
149A578THR00.0090.01334.200-0.158-0.1580.0000.0000.0000.000
150A579PRO00.0080.00534.0000.2550.2550.0000.0000.0000.000
151A580LEU0-0.0240.00428.2350.0480.0480.0000.0000.0000.000
152A581GLN00.0510.02230.1230.0710.0710.0000.0000.0000.000
153A582PHE00.0120.00023.5740.2750.2750.0000.0000.0000.000
154A583THR0-0.012-0.01825.604-0.417-0.4170.0000.0000.0000.000
155A584GLN00.037-0.00723.5480.2360.2360.0000.0000.0000.000
156A585GLY00.0080.01221.019-0.414-0.4140.0000.0000.0000.000
157A586LYS10.8200.90320.565-12.016-12.0160.0000.0000.0000.000
158A587TRP00.0070.01213.1910.4440.4440.0000.0000.0000.000
159A588TYR0-0.005-0.02118.270-1.206-1.2060.0000.0000.0000.000
160A589LEU00.0320.04115.8121.1641.1640.0000.0000.0000.000
161A590LEU0-0.045-0.03017.463-1.161-1.1610.0000.0000.0000.000
162A591THR00.0140.00117.6180.7220.7220.0000.0000.0000.000
163A592SER0-0.018-0.01319.460-0.719-0.7190.0000.0000.0000.000
164A593THR00.017-0.01120.2150.5260.5260.0000.0000.0000.000
165A594VAL0-0.026-0.00421.443-0.524-0.5240.0000.0000.0000.000
166A595MET0-0.0260.01024.1420.0830.0830.0000.0000.0000.000
167A596HIS0-0.0020.00222.8130.3330.3330.0000.0000.0000.000
168A597ASP-1-0.824-0.90826.3579.4449.4440.0000.0000.0000.000
169A598GLY00.0340.02927.3140.3210.3210.0000.0000.0000.000
170A599PRO00.0410.01225.9120.0160.0160.0000.0000.0000.000
171A600THR0-0.006-0.01021.6520.0550.0550.0000.0000.0000.000
172A601SER00.0310.01820.0680.3990.3990.0000.0000.0000.000
173A602SER0-0.016-0.01017.3200.6420.6420.0000.0000.0000.000
174A603GLY00.0310.01813.590-0.165-0.1650.0000.0000.0000.000
175A604TRP00.0310.01411.074-0.322-0.3220.0000.0000.0000.000
176A605VAL0-0.034-0.02613.715-0.508-0.5080.0000.0000.0000.000
177A606TRP00.0290.02413.247-0.131-0.1310.0000.0000.0000.000
178A607MET0-0.006-0.00918.147-0.585-0.5850.0000.0000.0000.000
179A608ASN00.0770.05021.3390.5010.5010.0000.0000.0000.000
180A609GLN0-0.014-0.00623.787-0.317-0.3170.0000.0000.0000.000
181A610GLU-1-0.816-0.90925.8839.5849.5840.0000.0000.0000.000
182A611LEU00.0190.01626.469-0.080-0.0800.0000.0000.0000.000
183A612THR0-0.010-0.00329.440-0.343-0.3430.0000.0000.0000.000
184A613ASN00.015-0.01332.2460.1870.1870.0000.0000.0000.000
185A614ASN0-0.0010.00135.824-0.092-0.0920.0000.0000.0000.000
186A615ILE0-0.0030.02131.130-0.103-0.1030.0000.0000.0000.000
187A616ALA0-0.0060.00833.3060.0770.0770.0000.0000.0000.000
188A617TYR00.0420.01426.9690.1060.1060.0000.0000.0000.000
189A618ARG10.8450.91326.653-10.816-10.8160.0000.0000.0000.000
190A619VAL00.0660.03225.8490.2310.2310.0000.0000.0000.000
191A620ASP-1-0.770-0.84020.82913.66713.6670.0000.0000.0000.000
192A621PRO00.0720.00418.493-0.148-0.1480.0000.0000.0000.000
193A622GLY00.0310.01818.7150.4080.4080.0000.0000.0000.000
194A623MET0-0.057-0.02219.457-0.119-0.1190.0000.0000.0000.000
195A624MET0-0.043-0.02422.744-0.388-0.3880.0000.0000.0000.000
196A625TYR0-0.013-0.01019.629-0.112-0.1120.0000.0000.0000.000
197A626LEU0-0.0050.00722.729-0.088-0.0880.0000.0000.0000.000
198A627ILE0-0.020-0.01026.718-0.345-0.3450.0000.0000.0000.000
199A628THR00.020-0.00429.882-0.423-0.4230.0000.0000.0000.000
200A629PRO0-0.037-0.00528.1570.3320.3320.0000.0000.0000.000
201A630PRO0-0.0070.01924.079-0.253-0.2530.0000.0000.0000.000
202A631PRO00.0180.01227.064-0.049-0.0490.0000.0000.0000.000
203A632ALA00.0360.01526.7220.3970.3970.0000.0000.0000.000
204A633ALA0-0.034-0.02125.356-0.316-0.3160.0000.0000.0000.000
205A634SER0-0.048-0.01724.9710.2330.2330.0000.0000.0000.000
206A635GLN00.003-0.02619.3360.3480.3480.0000.0000.0000.000
207A636LEU0-0.027-0.00418.589-0.443-0.4430.0000.0000.0000.000
208A637TYR0-0.043-0.03612.9630.8800.8800.0000.0000.0000.000
209A638PHE0-0.042-0.02512.908-0.639-0.6390.0000.0000.0000.000
210A639GLU-1-0.788-0.8649.54122.87122.8710.0000.0000.0000.000
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212A641HIS0-0.011-0.0104.5835.4235.482-0.001-0.039-0.0190.000
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